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<h1>Online database search</h1>

<h2>Description</h2>

<p>
    This module allows identification of peaks or whole peak lists using an on-line compound database.
    Databases are queried for the calculated neutral mass of the peak and matching compounds are returned.
</p>

<p>
    Selection of peak for identification:<br>
    <img src="OnlineDBSearch_choose.png">
</p>

<p>
    Results of database query:<br>
    <img src="OnlineDBSearch_results.png">
</p>

<p>
    Displaying the structure of the database compound:<br>
    <img src="OnlineDBSearch_structure.png">
</p>

<h4>Method parameters</h4>
<dl>
    <dt>Database</dt>
    <dd>On-line database to search (see below)</dd>

    <dt>Peak m/z</dt>
    <dd>Detected m/z value of the peak. This is set automatically according to the peak subjected to identification.
    </dd>

    <dt>Charge</dt>
    <dd>Charge of the peak being identified. This value is used to calculate the neutral mass.</dd>

    <dt>Ionization method</dt>
    <dd>Type of ionization that produced the peak subjected to identification. This is used to calculate the neutral
        mass.
    </dd>

    <dt>Neutral mass</dt>
    <dd>This value is automatically calculated from the parameters above. The neutral mass represents the final search
        term for querying the on-line database.
    </dd>

    <dt>Number of results</dt>
    <dd>Limit for the number of results to be retrieved from the on-line database.</dd>

    <dt>Mass tolerance</dt>
    <dd>Tolerance of the neutral mass for searching the database.</dd>

    <dt>Isotope pattern filter</dt>
    <dd>If selected, only results which fit the required isotope pattern similarity score will be returned.</dd>

    <dt>Isotope pattern score threshold</dt>
    <dd>The score required for the isotope pattern filter.</dd>

</dl>


<h2>On-line databases</h2>

<p>
    Currently supported databases are listed below.
    Support for other databases may be implemented as additional plugins.
</p>

<h3>PubChem</h3>

<p>
    PubChem database (<a href="http://pubchem.ncbi.nlm.nih.gov/">http://pubchem.ncbi.nlm.nih.gov/</a>) contains millions
    of chemical compound structures.
</p>

<h3>KEGG</h3>

<p>
    KEGG database (<a href="http://www.genome.jp/kegg/">http://www.genome.jp/kegg/</a>) contains metabolites and other
    biomolecules present in natural metabolic pathways.
</p>


<h3>HMDB</h3>

<p>
    The Human Metabolome Database (HMDB) (<a href="http://www.hmdb.ca/">http://www.hmdb.ca/</a>) contains over 7,000
    known metabolites found in human body.
</p>

<h3>YMDB</h3>

<p>
    The Yeast Metabolome Database (YMDB) (<a href="http://www.ymdb.ca">http://www.ymdb.ca</a>) is a manually curated
    database of small molecule metabolites found in or produced by <i>Saccharomyces cerevisiae</i>
    (also known as Baker’s yeast and Brewer’s yeast).
</p>

<h3>ChemSpider</h3>

<p>
    The ChemSpider database (<a href="http://www.chemspider.com/">http://www.chemspider.com/</a>) contains over 67
    million compounds. To search ChemSpider you must provide a "Security key" from your ChemSpider API account.
    If you don't have an account, please register at <a href="https://developer.rsc.org">https://developer.rsc.org</a>.
</p>

<h3>PlantCyc</h3>

<p>
    The Plant metabolic pathway database (<a href="http://plantcyc.org">http://plantcyc.org</a>) provides access
    to manually curated or reviewed information about shared and unique metabolic pathways present 
    in over 350 plant species.
</p>


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